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44.64944649446495 ] }, { "contrast": "genomic_hprc_asian minus genomic", "verdict": "negative aggregate difference in this tested configuration", "pairs": 541, "difference_pp": -8.317929759704251, "interval": [ -11.41804788213628, -5.37037037037037 ] }, { "contrast": "genomic_core_hprc_asian minus genomic", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 541, "difference_pp": -0.7393715341959335, "interval": [ -1.8281535648994516, 0.18726591760299627 ] }, { "contrast": "genomic_core_hprc_asian minus genomic_core_nonasian", "verdict": "positive aggregate difference in this tested configuration", "pairs": 541, "difference_pp": 3.142329020332717, "interval": [ 1.308411214953271, 5.018587360594796 ] }, { "contrast": "genomic_core_hprc_asian minus genomic_hprc_asian", "verdict": "positive aggregate difference in this tested configuration", "pairs": 541, "difference_pp": 7.578558225508318, "interval": [ 4.562043795620438, 10.674157303370787 ] }, { "contrast": "GRAPH_RETRIEVAL_ABLATION.json hprc/E3 union minus native-only", "verdict": "positive aggregate difference in this tested configuration", "pairs": 377, "difference_pp": 2.387267904509284, "interval": [ 0.5333333333333333, 4.370179948586118 ] }, { "contrast": "GRAPH_RETRIEVAL_ABLATION.json hprc_asian/E3 union minus native-only", "verdict": "positive aggregate difference in this tested configuration", "pairs": 377, "difference_pp": 3.4482758620689653, "interval": [ 1.0582010582010581, 5.974025974025974 ] }, { "contrast": "GRAPH_GENOMIC_RETRIEVAL_ABLATION.json hprc/E3 union minus native-only", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 541, "difference_pp": -0.9242144177449169, "interval": [ -2.536231884057971, 0.7233273056057866 ] }, { "contrast": "GRAPH_GENOMIC_RETRIEVAL_ABLATION.json hprc_asian/E3 union minus native-only", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 541, "difference_pp": 0.5545286506469501, "interval": [ -0.7352941176470589, 1.8796992481203008 ] }, { "contrast": "dsf100 hprc linked minus independent", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 377, "difference_pp": 0.26525198938992045, "interval": [ -1.5915119363395225, 2.1220159151193636 ] }, { "contrast": "dsf100 hprc linked minus shuffled", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 377, "difference_pp": 0.0, "interval": [ -2.099737532808399, 2.1164021164021163 ] }, { "contrast": "dsf100 hprc_asian linked minus independent", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 377, "difference_pp": 0.26525198938992045, "interval": [ -1.5831134564643798, 2.1563342318059298 ] }, { "contrast": "dsf100 hprc_asian linked minus shuffled", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 377, "difference_pp": -0.26525198938992045, "interval": [ -2.1220159151193636, 1.6129032258064515 ] }, { "contrast": "dsf250 hprc linked minus independent", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 377, "difference_pp": 0.0, "interval": [ -1.2987012987012987, 1.3054830287206267 ] }, { "contrast": "dsf250 hprc linked minus shuffled", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 377, "difference_pp": 0.0, "interval": [ -1.0554089709762533, 1.0638297872340425 ] }, { "contrast": "dsf250 hprc_asian linked minus independent", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 377, "difference_pp": 0.0, "interval": [ -1.3404825737265416, 1.5706806282722514 ] }, { "contrast": "dsf250 hprc_asian linked minus shuffled", "verdict": "no clear aggregate evidence under both family interval and sign-flip checks", "pairs": 377, "difference_pp": -0.26525198938992045, "interval": [ -1.5873015873015872, 1.0810810810810811 ] }, { "contrast": "unnamed recovery: genomic_hprc minus genomic_nonasian", "verdict": "positive aggregate difference in this tested configuration", "pairs": 175, "difference_pp": 26.285714285714285, "interval": [ 18.96551724137931, 34.193548387096776 ] }, { "contrast": "unnamed recovery: genomic_hprc_asian minus genomic_nonasian", "verdict": "positive aggregate difference in this tested configuration", "pairs": 175, "difference_pp": 31.428571428571427, "interval": [ 23.863636363636363, 39.24050632911393 ] }, { "contrast": "unnamed recovery: genomic_hprc_asian minus genomic_hprc", "verdict": "positive aggregate difference in this tested configuration", "pairs": 175, "difference_pp": 5.142857142857143, "interval": [ 1.7647058823529411, 8.938547486033519 ] }, { "contrast": "unnamed recovery: genomic_hprc_asian minus genomic", "verdict": "positive aggregate difference in this tested configuration", "pairs": 175, "difference_pp": 34.857142857142854, "interval": [ 27.564102564102566, 42.42424242424242 ] }, { "contrast": "unnamed recovery: genomic_core_hprc_asian minus genomic_core_nonasian", "verdict": "positive aggregate difference in this tested configuration", "pairs": 175, "difference_pp": 20.0, "interval": [ 13.793103448275861, 26.630434782608695 ] }, { "contrast": "unnamed recovery: genomic_core_hprc_asian minus genomic", "verdict": "positive aggregate difference in this tested configuration", "pairs": 175, "difference_pp": 22.285714285714285, "interval": [ 15.853658536585366, 29.069767441860463 ] }, { "contrast": "DogoHLA_genomic/hprc/E1 minus full-genomic IPD", "verdict": "negative aggregate difference in this tested configuration", "pairs": 541, "difference_pp": -9.611829944547136, "interval": [ -12.86231884057971, -6.4935064935064934 ] }, { "contrast": "DogoHLA_genomic/hprc/E2 minus full-genomic IPD", "verdict": "negative aggregate difference in this 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Missing runs remain availability gaps, never no-calls.", "Numeric fields ignore expression suffix; ambiguous labels collapse only when every alternative agrees at requested resolution. No shorter-field padding.", "SpecHLA3.65 annotation retains3.38 mapping/binning. OptiType bundled database supports classI two-field. HLA*LA uses historical native graph and current3.65 G-name expansion, not identity-certified historical nomenclature.", "HLA*LA G groups ambiguous at2field remain unresolved. Native G output does not support a four-field comparison; no HLA*LA four-field denominator is created. Separate G endpoint compares both methods after current3.65 group projection; shorter names project only when every current descendant agrees on a G group.", "Incomplete family metadata uses explicitly reported singleton fallback; fallback does not certify independence.", "Family-cluster bootstrap4000 and exact/MonteCarlo family sign-flip from interpretation score_ablation. 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excludes unnamed truth.", "- The current graph caller selects observed candidate paths. It cannot", " synthesize an allele absent from every candidate, even if some of its", " component variation is in the graph. Missing-catalogue failures are", " therefore distinct from mapping or inference failures.", "- Graph retrieval can help particular loci; aggregate gains must survive", " the native-only placement control and the strong genomic baseline.", "- Regional recruitment starts from linear-reference MHC, alternative", " and HLA alignments, with mate rescue. Graph inference cannot recover", " pairs discarded at recruitment. These tests therefore do not measure", " a possible benefit of graph-based recruitment from the full WGS.", "- A null LD result applies to the tested prior, read evidence and depths.", " It does not establish absence of biological linkage disequilibrium.", "- DRB1 dominates many unmatched counts. Exact annotation-core matches", " need independent raw-read/boundary validation before novelty claims.", "- All comparisons remain developmental. Multiple modes and diagnostic", " endpoints are reported rather than selecting the best result.", "", "6. Supported-resolution comparator benchmarks", "OptiType/SpecHLA use two-field comparisons; HLA*LA uses common G classes.", "Unresolved numeric projections of HLA*LA G classes are not wrong two-field calls.", "SpecHLA uses 3.65 annotation with 3.38 mapping/binning; OptiType", "uses its bundled class-I database; HLA*LA uses its historical graph.", "They are not fully matched 3.65-database benchmarks.", "Detailed locus, region and stricter-resolution results: baseline-completion-20261020/A3_SCORES.txt.", "optitype: completed donors=86/86; two-field correct=217/245; called=218; matched with genomic T1K=245 eligible pairs.", " optitype minus genomic T1K: -9.80pp; CI95=[-13.934426229508198, -5.761316872427984]; family p=4.9998e-05.", "spechla: completed donors=86/86; two-field correct=514/552; called=552; matched with genomic T1K=552 eligible pairs.", " spechla minus genomic T1K: -5.25pp; CI95=[-7.592592592592593, -3.1135531135531136]; family p=4.9998e-05.", "hlala: completed donors=86/86; common-G correct=505/552; called=531; matched with genomic T1K=552 eligible pairs.", " hlala minus genomic T1K: -8.51pp; CI95=[-10.564663023679417, -6.545454545454546]; family p=4.9998e-05.", "HLA-HD remains blocked by unavailable distribution; no access-request message was sent.", "", "Broader research plan disposition:", "- HLA_LA: All86 common-G baseline complete; historical graph and label-resolution limitations remain; see A3 receipts", "- HLA_HD_SpecHLA_OptiType: SpecHLA and OptiType all86 supported-resolution benchmarks complete; HLA-HD distribution unavailable; see A3 status", "- truth_raw_HiFi_QC: Not yet certified; assembly-based endpoints exploratory", "- untouched_confirmatory_set: Not frozen/admitted", "- matched_DeepVariant_variant_H2: Not implemented/run; old vg/bcftools results confounded", "- fold_safe_RCCX_H3: Not yet rebuilt/scored", "- novel_recombinant_simulation_H1: Not yet implemented/run" ] }